an advanced chemical viewer for single and multiple chemical structures, queries and reactions

Table viewer for 2D/3D structures, reactions and their associated data. Supporting all common chemistry file formats and some document formats, such as .doc and .pdf, where chemical text names and context are extracted into a MarvinView table.

Product Type:application
Interfaces:CLIGUI ( Desktop )API ( Java, .NET )

Advanced visualization

Visualization of databases

Using a simple renderer tens of thousands molecules can be quickly displayed in a spreadsheet or matrix layout. Additional fields, molecule name, generated IUPAC name and SMILES string can also be visualized.

Reaction Drawing

Display and formatting

MarvinView can visualize various atom properties such as atom numbers, lone pairs, atom mapping, graph invariants and R-groups. 2D and 3D coordinates can be rendered in various ways such as ball and stick, wireframe and space filling. Saving chemical structures as Web or camera ready resolution images, in various formats is also supported.

Reaction Drawing

The power of ChemAxon’s Calculator Plugin’s directly on the canvas

Calculator Plugins offer a solution to a wide range of problems faced by medicinal or computational chemists. ChemAxon’s Calculator Plugin suite is a cheminformatics toolkit to calculate structure based properties and gives unmatched versatility and power in characterizing your structures. Through Chemical Terms, a language to parameterize and combine Calculator Plugin results, you can quickly see a range of relevant properties and arguments for the structure or structures on the canvas as you are creating.

Predictors and Enumerators

ChemAxon’s software offers fast and accurate predictions of basic physicochemical properties such as logP, logD, pKa. Multiple stereoisomers and tautomers of each input structure according to user-specified limits can also be generated. Since a significant fraction of drug-like molecules are weak acids or bases with multiple low-energy ionization or tautomeric states fast and accurate or most likely structures is useful.

Molecular descriptors

Calculating molecular descriptors include; topological indices, structural keys, indices, physical properties, topological polar surface area or molecular surface area descriptors with wide applicability to both biological activity and ADME property prediction. Descriptors can also be used for classification, clustering, filtering and predictive model construction.

Molecular Modelling

ChemAxon offers a streamlined interface for interactive molecular mechanics applications such as 3D ligand optimization, conformation generation. Easy use of 3D alignment and Molecular Dynamics makes it invaluable for both computational and medicinal chemists. Partial charge distribution and its derivatives determine many physicochemical properties of a molecule such as reactivity or pharmacophore pattern and can called from the interface.

Chemical feature parade

Welcome to the widest support for chemical structure file formats

In addition to relevant standard file types MarvinView can open protein, nucleic acid sequence files, Gaussian input and output files, chemical name file formats, JChem Table files. ChemDraw and Symyx Draw file formats are also recognized by Marvin. In the IP space Marvin users can also import Markush DARC files and save all features within Marvin’s default (mrv) format for sharing and subsequent editing. Marvin can import and export single and multiple molecules. Image files can be converted in MarvinSketch using the free OSRA application.

Editing chemical structures

MarvinView offers a basic toolkit to edit chemical structures such as 2D/3D cleaning, aromatic form conversion, contracting/expanding abbreviated groups and regenerating bonds, adding/removing explicit H atoms. For more extensive editing users can open the structure within MarvinSketch and then return to MarvinView.

Reaction Drawing

Batch calculations and file format conversion using MolConverter

MolConverter is a command line program in Marvin Beans and JChem that converts between various file types. Operating in batch mode users can specify various documents, molecule files, graphic and compression/encoding formats. When handling chemical structures users can specify how to handle chemical features relevant to molecule file formats.

Articles in the library

The challenges of loading chemical supplier catalogues

May 20, 2010 - Presentation
We will describe the “fun” we are having creating rules and workflows to tidy up the data from chemical supplier catalogues for our compound sourcing database.
Author: ()

A chemistry friendly system integrating drug design tools and a consistent v…

Sep 26, 2014 - Presentation
Drug discovery today is challenging with metabolism and toxicity playing key roles. Here we present a web based system
Author: ()

Macromolecular Structure Notation, Editing and Registration

Sep 16, 2009 - Presentation
While many software systems exist for small molecule structure representation, drawing and registration and are widely used by biotech/pharmaceutical companies in small molecule drug disc…

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